Dear Vince,
I checked and found the version 1.0 of pyMSMT released online (
https://github.com/Amber-MD/pymsmt/releases/tag/v1.0 <
https://github.com/Amber-MD/pymsmt/releases/tag/v1.0>) could be compatible with Amber11, Amber12, and Amber14. It uses a periodic table in ParmEd and the path of that periodic table doesn’t change between these versions and AmberTools15. So you can try to install this version on your computer.
Kind regards,
Pengfei
> On Apr 9, 2016, at 10:29 AM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> Dear Vince,
>
> MCPB.py is only available in AmberTools15 or higher version. It may not be compatible with Amber12 and AmberTools14. Here is a tutorial about MCPB.py: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
>
> There is updated version of MCPB.py based on the one in AmberTools15 you can download from here: https://github.com/Amber-MD/pymsmt/releases <https://github.com/Amber-MD/pymsmt/releases>.
>
> If you have any questions, please tell me.
>
> Kind regards,
> Pengfei
>
>> On Apr 8, 2016, at 7:42 PM, Vasantha Kumar <vin.vasanth.gmail.com <mailto:vin.vasanth.gmail.com>> wrote:
>>
>> Dear David
>>
>> My peptide is modified, 2HIS (mutated) and 2CYS (regular) coordinated to
>> zinc (II) ion. As per the ZAFF model to handle zinc works well for 20ps rMD
>> nmr structure calculation and metal geometry is fine. When I change the
>> total time of rMD to 40ps or higher then metal geometry shows deviation.
>>
>> Is this MCPB.py is compatible is compatible with amber 12, amber tool 14.?
>> I would like to give a try with MCPB.py method, therefore I kindly request
>> you to provide me email contact of the author of MCPB.py, so that I can
>> request related files to handle metal ion. That would be helpful to solve
>> my problem with metal coordination geometry.
>>
>> thank you,
>> Vince
>>
>> 2016-04-09 1:29 GMT+02:00 Vasantha Kumar <vin.vasanth.gmail.com <mailto:vin.vasanth.gmail.com>>:
>>
>>> Dear Calos
>>>
>>> GB implicit solvent model with IG=5
>>>
>>> Bonds between 2HIS and 2CYS to Zinc metal ion (II), as described in ZAFF
>>> model. I also followed same protocol. For shorter rMD (20ps) coordination
>>> geometry wont change much and I gave tetrahedral geometry, but if I change
>>> rMD total time 40 or 100ps then metal geometry changes. However geometry
>>> visually close to tetrahedral geometry, but when I check in chimera, the
>>> pdbs from 40 or 100ps rMD showed deviation (trigonal bi-pyramidal) in the
>>> metal geometry and not tetrahedral geometry in 20ps rMD.
>>>
>>> thank you
>>> Vince
>>>
>>>
>>>
>>>
>>> 2016-04-08 17:01 GMT+02:00 David Cerutti <dscerutti.gmail.com <mailto:dscerutti.gmail.com>>:
>>>
>>>> I think the "bond between ligands were defined" means he is trying to use
>>>> harmonic NMR restraints between atoms to mimic the effect of actual
>>>> topological harmonic bonds. What
>>>> you need, Vince, is Metal Center Parameter Builder (MCPB.py). This
>>>> facility is part of the next release of Amber, but you can get it from its
>>>> author in my lab. This will automate the quantum calculations to
>>>> distribute the charges of the metal center over the atom itself and the
>>>> coordinating groups, estimate force constants for bonds that connect the
>>>> metal to the rest of the system, and also fill in force constants for the
>>>> new angle terms that forming the new bonds implies. MCPB.py will print a
>>>> frcmod file and library to feed to tleap so that it knows about your new
>>>> "residue" in the metal center. Once Amber knows that these bonds and
>>>> angles actually exist, it will count the correct exclusions so that your
>>>> simulaion no longer has the metal center crashing into atoms to which it
>>>> is
>>>> bonded. This is what the NMR restraints are not able to do for you.
>>>>
>>>> Dave
>>>>
>>>>
>>>> On Fri, Apr 8, 2016 at 10:32 AM, Carlos Simmerling <
>>>> carlos.simmerling.gmail.com <mailto:carlos.simmerling.gmail.com>> wrote:
>>>>
>>>>> I don't know which GB model you are using, but I expect that they will
>>>> not
>>>>> work well for many ions, especially ones that are not monovalent. I'm
>>>> not
>>>>> sure I understand the rest of your email about "bond between ligands
>>>> were
>>>>> defined".
>>>>>
>>>>> On Fri, Apr 8, 2016 at 9:13 AM, Vasantha Kumar <vin.vasanth.gmail.com <mailto:vin.vasanth.gmail.com>>
>>>>> wrote:
>>>>>
>>>>>> Dear AMEBR users
>>>>>>
>>>>>> Is it possible to obtain proper tetrahedral metal geometry for a
>>>> modified
>>>>>> peptide, whose structure was calculated using nmr restraints and using
>>>>>> AMBER in restrained MD method.
>>>>>> I am currently using non-boded ZAFF model to handle zinc. In my
>>>>> calculation
>>>>>> of 200ps rMD in GB model metal geometry is deviated from ideal
>>>> geometry
>>>>>> (tetrahedral to trigonal bipyramidal). For the moment I have removed
>>>> the
>>>>>> nmr restraints in the coordination, because on the ligand peaks was
>>>> not
>>>>>> identified due to sever overlap and since bond between ligands were
>>>>>> defined. Could any one suggest me in solution NMR structure is it
>>>>> possible
>>>>>> to maintain geometry in rMD protocol.
>>>>>>
>>>>>> thanks in advance
>>>>>> Vince
>>>>>> _______________________________________________
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>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>> _______________________________________________
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>>>>>
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>>>
>>>
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Received on Sat Apr 09 2016 - 20:00:04 PDT
